Home LiteratureArticle Details
PMID: 21966348 Published · ppublish English Journal Article

Structural Chemistry of Human SET Domain Protein Methyltransferases.

Current chemical genomics ·Vol. 5 ·No. Suppl 1 ·2011-00-00 ·Pages 85-94

Schapira M

Abstract

There are about fifty SET domain protein methyltransferases (PMTs) in the human genome, that transfer a methyl group from S-adenosyl-L-methionine (SAM) to substrate lysines on histone tails or other peptides. A number of structures in complex with cofactor, substrate, or inhibitors revealed the mechanisms of substrate recognition, methylation state specificity, and chemical inhibition. Based on these structures, we review the structural chemistry of SET domain PMTs, and propose general concepts towards the development of selective inhibitors.

Keywords
Methyltransferase PMT SET domain epigenetics. histone structure
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Schapira Matthieu
Structural Genomics Consortium, University of Toronto, MaRS Centre, Toronto, Ontario, M5G 1L7, Canada.
References (43)
43 references, click to expand
  1. Identifying and characterizing binding sites and assessing druggability.
    J Chem Inf Model. 2009 Feb;49(2):377-89 PMID: 19434839
  2. Structural origins for the product specificity of SET domain protein methyltransferases.
    Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20659-64 PMID: 19088188
  3. Specificity and mechanism of the histone methyltransferase Pr-Set7.
    Genes Dev. 2005 Jun 15;19(12):1444-54 PMID: 15933069
  4. Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation.
    Blood. 2011 Feb 24;117(8):2451-9 PMID: 21190999
  5. The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules.
    Nat Struct Mol Biol. 2008 Mar;15(3):245-50 PMID: 18264113
  6. The emerging therapeutic potential of histone methyltransferase and demethylase inhibitors.
    ChemMedChem. 2009 Oct;4(10):1568-82 PMID: 19739196
  7. A novel arginine methyltransferase inhibitor with cellular activity.
    Bioorg Med Chem Lett. 2007 Aug 1;17(15):4150-3 PMID: 17570663
  8. Chemical mechanisms of histone lysine and arginine modifications.
    Biochim Biophys Acta. 2009 Jan;1789(1):45-57 PMID: 18603028
  9. Trimethylation of histone H3 lysine 4 impairs methylation of histone H3 lysine 9: regulation of lysine methyltransferases by physical interaction with their substrates.
    Epigenetics. 2010 Nov-Dec;5(8):767-75 PMID: 21124070
  10. The diverse functions of histone lysine methylation.
    Nat Rev Mol Cell Biol. 2005 Nov;6(11):838-49 PMID: 16261189
  11. Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks.
    Mol Cell. 2009 Jan 30;33(2):181-91 PMID: 19187761
  12. G9a and Glp methylate lysine 373 in the tumor suppressor p53.
    J Biol Chem. 2010 Mar 26;285(13):9636-9641 PMID: 20118233
  13. Chromatin modifications and their function.
    Cell. 2007 Feb 23;128(4):693-705 PMID: 17320507
  14. Toward the development of potent and selective bisubstrate inhibitors of protein arginine methyltransferases.
    Bioorg Med Chem Lett. 2010 Apr 1;20(7):2103-5 PMID: 20219369
  15. Structural basis of EZH2 recognition by EED.
    Structure. 2007 Oct;15(10):1306-15 PMID: 17937919
  16. In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases.
    J Biol Chem. 2005 Feb 18;280(7):5563-70 PMID: 15590646
  17. Structural biology of human H3K9 methyltransferases.
    PLoS One. 2010 Jan 11;5(1):e8570 PMID: 20084102
  18. Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity.
    Proc Natl Acad Sci U S A. 2007 May 22;104(21):8797-802 PMID: 17517655
  19. Structure and catalytic mechanism of the human histone methyltransferase SET7/9.
    Nature. 2003 Feb 6;421(6923):652-6 PMID: 12540855
  20. Structural basis for the product specificity of histone lysine methyltransferases.
    Mol Cell. 2003 Jul;12(1):177-85 PMID: 12887903
  21. SET domain protein lysine methyltransferases: Structure, specificity and catalysis.
    Cell Mol Life Sci. 2006 Dec;63(23):2755-63 PMID: 17013555
  22. Protein methyltransferases as a target class for drug discovery.
    Nat Rev Drug Discov. 2009 Sep;8(9):724-32 PMID: 19721445
  23. Crystal structure and functional analysis of the histone methyltransferase SET7/9.
    Cell. 2002 Oct 4;111(1):105-15 PMID: 12372304
  24. Binary switches and modification cassettes in histone biology and beyond.
    Nature. 2003 Oct 2;425(6957):475-9 PMID: 14523437
  25. The SET-domain protein superfamily: protein lysine methyltransferases.
    Genome Biol. 2005;6(8):227 PMID: 16086857
  26. Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases.
    J Mol Biol. 2010 Jul 2;400(1):1-7 PMID: 20434463
  27. Structural chemistry of the histone methyltransferases cofactor binding site.
    J Chem Inf Model. 2011 Mar 28;51(3):612-23 PMID: 21366357
  28. Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
    Nat Struct Mol Biol. 2009 Mar;16(3):312-7 PMID: 19219047
  29. Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase.
    Cell. 2003 Mar 7;112(5):711-23 PMID: 12628190
  30. Structural basis for the methylation site specificity of SET7/9.
    Nat Struct Mol Biol. 2006 Feb;13(2):140-6 PMID: 16415881
  31. Many paths to methyltransfer: a chronicle of convergence.
    Trends Biochem Sci. 2003 Jun;28(6):329-35 PMID: 12826405
  32. Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas.
    Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):20980-5 PMID: 21078963
  33. Crystal structure of cardiac-specific histone methyltransferase SmyD1 reveals unusual active site architecture.
    J Biol Chem. 2010 Dec 24;285(52):40635-44 PMID: 20943667
  34. Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a.
    J Med Chem. 2009 Dec 24;52(24):7950-3 PMID: 19891491
  35. Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase.
    Genes Dev. 2005 Jun 15;19(12):1455-65 PMID: 15933070
  36. Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet.
    EMBO J. 2003 Jan 15;22(2):292-303 PMID: 12514135
  37. Uncovering the human methyltransferasome.
    Mol Cell Proteomics. 2011 Jan;10(1):M110.000976 PMID: 20930037
  38. Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase.
    Mol Cell. 2007 Feb 9;25(3):473-81 PMID: 17289593
  39. Protein lysine methyltransferase G9a acts on non-histone targets.
    Nat Chem Biol. 2008 Jun;4(6):344-6 PMID: 18438403
  40. Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9.
    Nat Chem Biol. 2005 Aug;1(3):143-5 PMID: 16408017
  41. Structural insights into the autoinhibition and posttranslational activation of histone methyltransferase SmyD3.
    J Mol Biol. 2011 Feb 11;406(1):149-59 PMID: 21167177
  42. The control of histone lysine methylation in epigenetic regulation.
    Biochimie. 2007 Jan;89(1):1-20 PMID: 16919862
  43. Structural genomics of histone tail recognition.
    Bioinformatics. 2010 Oct 15;26(20):2629-30 PMID: 20739309
Article Info
Journal
Current chemical genomics
Abbr.
Curr Chem Genomics
ISSN
1875-3973
Published
2011-00-00
Epub
2011-00-22
Pages
85-94
Language
English
Region
United Arab Emirates
NLM ID
101513465
PMCID
PMC3178901
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com